The aim of this study is to search a parameter which characterize the flow ability and analyze the contribution of diffusion to total mass flux of gas flow in pore of shale whose size is as low as nanoscale. The diffusion coefficient of the flow region which was determined by Kundsen number was taken as the diffusion coefficient of system, then it was substituted into the equation which describes gas diffusive and flow in nano-porous media, the apparent permeability and mass flux were calculated and the impacts of the pore radius and gas type were analyzed finally. The result showed that the diffusion of gas in shale was mainly in the transition diffusion or Fick diffusion region; The ratio of the apparent permeability of considering the diffusion and slippage effect to Darcy permeability and the ratio of diffusion mass flux to total mass flux increased with the decreasing of the pore radius; The diffusion ability of the methane was stronger than ethane’s. The present study implied that the calculated results of the diffusion coefficient which considers three kind of diffusion was less than that one considering Knudsen diffusion only; Considering diffusion and slippage effect, the apparent permeability of nanoscale pore of shale was 10-6 μm2 level, not 10-9 μm2 level in general temperature and pressure of shale reservoir.